Both names are really nice and would go great with Jake. Nathan is a little more popular, so Emmett gets a point for that. However, Nathan has the nickname Nate which I think is just adorable. Jake and Nate sounds kinda similar though so you have to think if that would bother you (or your two sons). If you really can't decide and don't have a middle name already picked out how about Nathan Emmett or Emmett Nathan? (Although Nathaniel Emmett/Emmett Nathaniel does flow better)